The current version of Qucs
(0.0.19 RC as of this writing) turns out to be an excellent educational
toy when it comes to S-parameters and the Smith chart.

Essentially, you need a "power source" for each port of your circuit.
This component looks like a voltage source with a series resistor
in one package. Next, you need an "S-parameter simulation".
This will automatically set up the matrix of N by N ports.
Once you compute the simulation, in the graphing tab you can
select the two versions of the Smith chart, or a "cartesian"
Bode plot. You will be offered the S-matrix members for use
in your charts/plots.